RAP1A p.Ala142=
c.426C>A · rs771755209 · VCV748010
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.135%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 6 | GERP 0.92, phastCons 1 |
| Overall | ||
| CADD | 14.75 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.135%
Admixed American · 81/59,926 alleles
Filtering AF
0.111%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.103%
Overall
0.00868%
140/1,613,556 alleles · rare
exomes 75/1,461,466 · genomes 65/152,090 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.135% | 740 |
| Middle Eastern | 0.0493% | 2,027 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,618 |
| European (non-Finnish) | 0.00424% | 23,596 |
| African / African-American | 0.00267% | 37,428 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- RAP1A
- Protein
- p.Ala142=
- Coding
- c.426C>A
- MANE Select
- NM_002884
- dbSNP
- rs771755209
- Type
- single nucleotide variant
- Location
- chr1:111704444 (GRCh38)
- Gene constraint
- LOEUF 0.433 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 92.17 · 4 PDB
- Residue 142
- a β-strand
Similar variants
- RAP1A c.126+185A>G Benign ★★ same type
- RAP1A c.57+176C>T Benign ★★ same type
- RAP1A c.57+29T>A Benign ★★ same type
- RAP1A c.57+45G>T Benign ★★ same type
- RAP1A c.58-48A>T Benign ★★ same type
- RAP1A c.*29+16C>T Benign ★★ same type
- RAP1A c.*29+97C>G Benign ★★ same type
- RAP1A p.Phe23= Likely benign ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/rap1a-p-ala142 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown